I wouldn't call the extinction of entire races a detail...
That one they could quite easily sidestep, as you don't really see it play out on screen. Also it was one of the sillier aspects of Mass Effect 3. Sabotaging the genophage or the Quarians losing at Rannoch shouldn't cause either to immediately go extinct.
If there was ever a post-ME3 sequel in the Milky Way the way to go about it would be have the Quarians survive a defeat at Rannoch, but in reduced numbers, and still without a home world. In a post-Reaper War setting they'd still be aboard the Migrant Fleet if you chose the Geth. Have choosing the Quarians result in the Quarians fully settling Rannoch and their former colony worlds, with the Migrant Fleet disappearing.
A similar thing could be done with the Krogan. Curing the genophage results in the Krogan resettling some of their former colony worlds, a resurgent Krogan fleet, and a Krogan ambassador aboard the Citadel. Sabotaging the cure results in the Krogan still being stuck on Tuchanka and with the DMZ still in place.
As for the Geth, dialogue by the Catalyst would give the devs an easy out. The Catalyst mentions that in the Extended Cut that anything destroyed by the Crucible can be rebuilt, and he says specifically in response to a query about the weapons' effects on Synthetics. If the Quarians were chosen at Rannoch they could have a rogue Quarian faction rebuild the Geth in the war's aftermath. The rebuilt Geth however are isolationist, hiding in the Perseus Veil, and do no trust organics beyond their own creators. If peace was achieved but the Geth were lost in Destroy, the new Quarian government of Rannoch rebuilds the Geth rather than a faction that went rogue. The rebuilt Geth live in harmony with their creators on Rannoch in a relationship similar to the Drell with the Hanar, but are almost never seen outside of Quarian space. If Synthesis/Control and peace was achieved at Rannoch, the Geth and Quarians share Rannoch as equals with a single ambassador representing both factions interests on the Citadel. The Geth have more involvement outside Quarian space.
All of the above could be conveyed quite easily by dialogue and codex entries alone, and potential issues such as the variable states of Rannoch and the Migrant Fleet can be avoided by not having either a location that you'll visit. The galaxy is a big place, and the series should seek to avoid continually revisiting the same locations repeatedly (outside the Citadel) anyway.
Quarian exosuits can be handled either by having the Quarians in all outcomes keeping their familiar exosuits, with them having become a part of Quarian culture even if Rannoch is settled, or by having the Quarians going unmasked in all outcomes. With the latter the Quarians would need to master some means of bolstering their immune systems in the lab if they are still aboard the Migrant Fleet.